The storyline is that you find Pandaria by shipwreck. Obviously this is before shipping routes are opened up to the zone.
So the solution might be to have something like Twilight Highlands initially, where you are personally using a portal to go back and forth while waiting for a base to be built.
But I think the best option would be to just do what they do in TH and have some initial quests which end with a small dock being built and repairs to a ship/zeppelin so you can get back. And then in 5.1, those little bases are turned into fortresses and harbors.